Habitats for soil microbiology

Most microbes need regular inputs of organic matter (e.g. plant residue) into the soil.
Larger soil organisms such as nematodes and insects need enough space to move through soil.
Most soil organisms require air, though some require a lack of oxygen. They live in low-oxygen micro-sites such as within soil aggregates. Generally, soil biological activity is enhanced by an increase in soil aeration.
It has been my experience that the best way to provide the long term benefits
of healthy soil are by adding organic matter and inoculants to the soil. A friend of mine likes to say it is a process, not an event.

Understanding the entire process is a life study for many people.http://ourenvironment.berkeley.edu/people_profiles/mary-firestone/
Mary Firestone Ph.D. Soil Microbiology Michigan State University is one exampleSoil microbial ecology: Microbial processing of carbon and nitrogen underlie the capacity of soil to support plant growth in agriculture, rangeland, forests, and wetlands. However the extreme heterogeneity of soil and the scale at which microorganisms interact with their habitat has made understanding the ecology of soil microbes a challenge of long duration.

Since beneficial microbes can live in the soil, so do disease-causing microbes live in the soil. I imagine that the various conditions, would be conducive to one set of microbes, while another set of conditions would promote the growth/proliferation of a different set of microbes...

So the $64000 question is:What cultural practices create the environment for the beneficials moreso than the pathos? Is water scheduling, an important part of the habitat's development?

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Now that I know that clay's texture(platelets) has nothing to do with water infiltration, percolation, or drainage,,, I wonder what does...
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Since beneficial microbes can live in the soil, so do disease-causing microbes live in the soil. I imagine that the various conditions, would be conducive to one set of microbes, while another set of conditions would promote the growth/proliferation of a different set of microbes...

So the $64000 question is:What cultural practices create the environment for the beneficials moreso than the pathos? Is water scheduling, an important part of the habitat's development?

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You are correct in that that beneficials & pathogens live in the soil and to a certain extent prefer different ecological situations.

There are many ways of tweaking the soil environment. There is no simple or single way to answer your question. We can certainly discuss in some detail here. But when do I get the $64,000?

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 Soil type dictates the number and characteristics of the microsites where soil organisms live.

 The diverse community of soil organisms is dynamic and interacts with both physical and chemical components of the soil habitat.

 The habitats in soil are changed by land management practices. ..."

While many articles like to engage in talking points about 'fertility', due to the byproducts of consuming decayers,, this one has some insight into 'habitat'... A possible starting point might be the idea that specific microsites that are desirable for specific organisms would be needed to provide a 'home' for those organisms...

One interesting highlight for me was the notion that bacteria are safer within soil aggregates than their typical existance on the surface of mineral soil particles...

Going on the assumption that beneficial bacteria are outcompeteing pathogenic bacteria, there should be a focus on what the pathgenics find to be an uncomfortable habitat...

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Now that I know that clay's texture(platelets) has nothing to do with water infiltration, percolation, or drainage,,, I wonder what does...
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Perhaps 'Red Thread" would be an enlightening study, since it lives outside the plants and grows in a specific type environment...

Any 'detailed' research done on, red thread, that makes it a little clearer what is actually taking place with the soil , that causes this organism to 'take off' across a lawn???

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Pick another example. I don't think think Red Thread is a soil borne disease. It certainly isn't spread through the soil.

Red thread is a disease of slow growing turf. Red thread is easily recognized by the red to coral-pink fungal strands (stromata) produced on leaf blades and sheaths. When turf is wet, the fungal stroma looks gelatinous and fleshy. As the grass dries, the stroma also dries and becomes thin and thread-like. Infected turf often appears to be suffering from lack of water, often times symptoms resemble dollar spot. Under close examination of the grass blades reveals red to coral-pink stromata. Under conditions of high humidity, pink cottony flocks of arthroconidia can be seen in the patches. Red thread occurs is favored by high humidity at temperatures between 60°-90° F (15.5° and 32° C). Cool, drizzly days of spring and fall are ideal for the development, and the disease spreads from plant to plant by growth of the stromata. These can be spread by wind, and mechanical equipment.http://www.msuturfdiseases.net/details/_/red_thread_14/

The fungi overwinter as a dried gelatinous mycelium covering on infected dead leaves or in clipping debris from previously infected plants.The fungi spread by transport of mycelium or infected leaves to new areas. The mycelium on living, infected plants are easily broken loose and transported mechanically. Fungi enter leaves through natural openings and cut tips, and spread rapidly through the remainder of the leaf. Red thread and pink patch diseases develop more readily when air temperatures are 65° to 75°F, with prolonged periods of rainy or humid weather. At times, the disease occurs in warmer, drier weather.http://cropsoil.psu.edu/turf/extension/factsheets/managing-diseases/red-thread